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phac-nml / staramr

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.
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Determine best approach to integrating typing information in staramr #59

Closed apetkau closed 5 years ago

apetkau commented 5 years ago

There are some different approaches to integrate typing information into the staramr reports.

1. Run outside of staramr

In this case we can run programs for MLST/organism identification outside of staramr (e.g,. in a Galaxy workflow) and integrate this information into the staramr report in Galaxy.

2. Run within staramr

We can have staramr run MLST or organism identification (e.g,. Mash) internally, and directly integrate into a report.

apetkau commented 5 years ago

We have decided to run MLST inside of staramr.